Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / alignment / AlignmentOutput.h

diff --git a/website/archive/binaries/mac/src/clustalw/src/alignment/AlignmentOutput.h b/website/archive/binaries/mac/src/clustalw/src/alignment/AlignmentOutput.h
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+/**
+ * Author: Mark Larkin
+ * 
+ * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
+ */
+/*
+ * The class AlignmentOutput is used to output the Alignment in all the different
+ * formats that have been selected. It will output all the different file types if
+ * these have been selected from the menu or the commandline.
+ * To use this class we must call openAlignmentOutput first. Then we call the function
+ * createAlignmentOutput with an Alignment to be output and the first and last sequence
+ * to be output as well. 
+ */
+#ifndef ALIGNMENTOUTPUT_H
+#define ALIGNMENTOUTPUT_H
+
+#include <string>
+#include <vector>
+#include <fstream>
+#include <memory>
+#include <sstream>
+#include <exception>
+#include <cassert>
+#include "Alignment.h"
+
+
+namespace clustalw
+{
+
+typedef struct rangeNum 
+{
+    int start;
+    int end;
+} rangeNum;
+
+typedef struct outputRegion 
+{
+    int _firstSeq;
+    int _lastSeq;
+    int _firstRes;
+    int _lastRes;
+} outputRegion;
+
+class AlignmentOutput
+{
+    public:
+        /* Functions */
+        AlignmentOutput();
+        bool openAlignmentOutput(string path);
+        bool QTOpenFilesForOutput(AlignmentFileNames fileNames);
+        void createAlignmentOutput(Alignment* alignPtr, int firstSeq, int lastSeq);
+        void printSecStructMask(int prfLength, vector<char>* mask, vector<char>* structMask);
+        /* Attributes */
+
+    private:
+        /* Functions */
+        void fastaOut(Alignment* alignPtr, outputRegion partToOutput);
+        void clustalOut(Alignment* alignPtr, outputRegion partToOutput);
+        void gcgOut(Alignment* alignPtr, outputRegion partToOutput);
+        void nexusOut(Alignment* alignPtr, outputRegion partToOutput);
+        void phylipOut(Alignment* alignPtr, outputRegion partToOutput);
+        void nbrfOut(Alignment* alignPtr, outputRegion partToOutput);
+        void gdeOut(Alignment* alignPtr, outputRegion partToOutput);
+        string nameonly(string s);
+        
+        void findRangeValues(Alignment* alignPtr, rangeNum *rnum, int firstRes, int lastRes, 
+                             int firstSeq);
+        bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
+        string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path, 
+                              string fileExtension);
+        int SeqGCGCheckSum(vector<char>* sequence, int length);
+        void showAlign();
+        /* Attributes */
+   
+        auto_ptr<ofstream> clustalOutFile;
+        auto_ptr<ofstream> gcgOutFile;
+        auto_ptr<ofstream> nbrfOutFile;
+        auto_ptr<ofstream> phylipOutFile;
+        auto_ptr<ofstream> gdeOutFile;
+        auto_ptr<ofstream> nexusOutFile;
+        auto_ptr<ofstream> fastaOutFile;
+        
+        string clustalOutName;
+        string gcgOutName;
+        string phylipOutName;
+        string nbrfOutName;
+        string gdeOutName;
+        string nexusOutName;
+        string fastaOutName;
+        vector<string> strongGroup; 
+        vector<string> weakGroup;
+        int clusSecStructOffset;
+        int clusSequenceOffset;        
+};
+
+}
+#endif
+